david abramson & hoang anh nguyen monash university
TRANSCRIPT
David Abramson &Hoang Anh Nguyen
Monash University
Background◦ Scientific Workflow◦ Tiled Display Wall◦ Why do we need a SWF-TDW link ?
Design and Implementation Case Study Conclusions & Future works
In-silico science (e-Science)◦ Complex process◦ Multiple steps in different computing environment
Scientific workflows◦ Help automate, manage and execute steps◦ Provide a high level, robust, repeatable research
environment.
SWF technology◦ Application of workflow technology to solve
scientific problems [1]◦ Different from Business Workflow
SWF Management System (SWFMS)◦ Specification, modification, run, re-run, and
monitoring of workflows Number of SWFMSs: Kepler, Taverna,
Triana, Vistrails, etc. Kepler was chosen to implement our
prototype
Built on top of Ptolemy II◦ Actor-oriented modelling◦ Vergil user-interface
Actor-oriented◦ Actors with input/output ports◦ Director
Powerful SWFMS◦ Web and grid-services support ◦ Provenance information
Figure 1: Sample Workflow in Kepler (source: [2])
What is a TDW ?◦ Visualization cluster◦ Multiple displays controlled by a powerful
computer/cluster◦ Acts like one or many virtual displays
TDW could be◦ Projectors◦ LCDs
Figure 2: Scalable Display Wall view from the back (Source [3])
Figure 3: An Optiportal at Monash Clayton ( Source [4] )
Built on top of Rocks Using SAGE, CGLX, COVISE as rendering
middleware SAGE: Scalable Adaptive Graphics
Environment◦ Open source◦ Distributed architecture: decouple graphic
rendering and graphic display
Figure 4: SAGE architecture
SAIL: Sage Application Interface Library
Sagereceiv
er
Sagereceiv
er
Sagereceiv
er
Sagereceiv
er
Sagereceiv
er
Sagereceiv
er
FreeSpace
Manager
FreeSpace
Manager
UI Client
UI Client
UI Client
UI Client
SAILSAIL
App 1App 1
SAILSAIL
App 2App 2 App 3App 3
SAILSAIL
SAGE messages
Pixel stream
Natural marriage◦ Computation and visualization
To date, no easy method connecting SWF to TDW.◦ Manual process◦ Did not receive a lot of attention from workflow
community
Goals:◦ Provide seamless link between SWFs and TDW◦ Middleware independence◦ Future user interactions
Design Alternatives◦ SSH actor◦ SAGE actor◦ Distributed architecture: dedicated server
SSH
pro
toco
lSSH
pro
toco
l Simple Inflexible
Simple Inflexible
SSH ActorSSH Actor
Figure 5: Solution using SSH actor
messages
Pixel stream
Sagereceive
r
Sagereceive
r
Sagereceive
r
Sagereceive
r
Sagereceiver
Sagereceiver
FreeSpaceManag
er
FreeSpaceManag
er
UI Client
UI Client
App App
SAILSAIL
SAGE actor
UI Client
UI Client
JNIJNIKepler code (Java)
Kepler code (Java)
SAILSAIL SAILSAIL
Figure 6: SAGE actor block diagram
compact possible feeding user feedbacks to workflow intensive computation on machine running Kepler middleware dependent
compact possible feeding user feedbacks to workflow intensive computation on machine running Kepler middleware dependent
Figure 7: Distributed Architecture
Server Interface
Server Interface
OptIPortalMiddlewar
e
OptIPortalMiddlewar
eServer
Interface
Server Interface
Server Interface
Server Interface
OptiServerOptiServer
OptIPortal
Kepler
OptIPortal Actor
OptIPortal Actor
OptIPortalMiddlewar
e
OptIPortalMiddlewar
e
OptIPortalMiddlewar
e
OptIPortalMiddlewar
e
middleware-independent highly distributed small communication overhead
middleware-independent highly distributed small communication overhead
Figure 8: Implementation
messages
Pixel stream
Sagereceiver
Sagereceiver
Sagereceiver
Sagereceiver
Sagereceiver
Sagereceiver
FreeSpaceManag
er
FreeSpaceManag
er
SAILSAIL
App 1
App 1
SAILSAIL
App 2
App 2
App 3
App 3
SAILSAIL
OptiUI Client
OptiUI Client
OptiServerOptiServer
Kepler OptIPortal Actor
OptIPortal Actor
Illustrate the ease of use with OptiportalActor
Use OptiportalActor in a set of optical microscopy workflows ◦ To visualize images of antibody cancer therapies*
Part of a larger project◦ Virtual microscopy◦ Demonstrating the utility of workflows for
microscopy
Developed in the Faculty of Medicine, Monash University
Fluorescent labeled antibodies, together with various reagents, are used to mark three distinct tissue types: ◦ tumour nuclei ◦ “stroma” or connective tissue◦ blood vessels that feed the tumour
These therapies work by denaturing the blood vessels to the tumor
Figure 9: Cancer Nuclei, Blood vessels, Stroma in confocal microscopy
Nuclei
Stroma
Blood vessels
Merged image
Figure 10: Confocal scanning workflow
Figure 11: Cancer image stack on Optiportal
Figure 12: Therapy effectiveness measurement workflow
Figure 13: Therapy effectiveness calculation on Optiportal
SWF-TDW linkage Demonstration the system with a case
study in optical microscopy To-dos
◦ Support more data-types (currently images and movies)
◦ Support other middleware◦ Support more interactive modes of operation:
computational steering environment.
[1] Lin, C., Lu, S., Lai, Z., Chebotko, A., Fei, X., Hua, J. and Farsha, F. “Service-oriented architecture for view: A visual scientific workflow management system.”, In SCC ’08: Proceedings of the 2008 IEEE International Conference on Services Computing, pages 335–342, Washington, DC, USA, 2008. IEEE Computer Society.
[2] https://kepler-project.org/users/copy_of_LotkaWorkflow.png/image_large [3] http://systems.cs.princeton.edu/omnimedia/images/back24.jpg [4] http://messagelab.monash.edu.au/Infrastructure/OptiPortal [5] http://www.sagecommons.org/images/stories/SAGEcomponents.jpg